Some of the files there are almost Programming Editor specific in that it's unlikely that other apps would have installed them, so it looks like the installer is doing something. The missing file may be a dependency which isn't needed because something else doesn't exist, or that may be a problem, it might be the same with versions which haven't been updated to later versions. Additionally, some files may perhaps only need installing for certain versions of Windows.
Apart from suggesting you uninstall, re-boot, install again, and see if that works, it may be time to take a deep breath and re-install windows from scratch. I consider it to be routine housework to re-install windows 98SE once every three to six months. You'll probably find it's far quicker to do that in the long term.